A transcript is available here in PDF. Note this statement in particular:

You mentioned earlier the possible significance of transposons. What part do you think they have played?

That is one of my many favourite topics. It is widely assumed – though not by everybody – that transposon-derived sequences are simply ‘selfish’ mobile genetic elements that have no function other than their own propagation. Books have been written about such things, and that is indeed one possibility. But the raw material for evolution is duplication and transposition, with the latter having the great advantage of being able to distribute functional cassettes. So it’s equally possible that a large fraction of the transposon-derived sequences that are in our genome are actually functional.

I have said it before, and I will say it again. The possibility that many transposable elements would be co-opted for organism-level functions has been around since the beginning of the “selfish DNA” idea. Moreover, the point of introducing the concept of selfish DNA in the first place was prompted by the standard assumption that just being present implied a function for all DNA.

“It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another.” (Orgel and Crick 1980)

“In our recent experience most people will agree, after discussion, that ignorant DNA, parasitic DNA, symbiotic DNA (that is, parasitic DNA which has become useful to the organism) and ‘dead’ DNA of one sort or another are all likely to be present in the chromosomes of higher organisms. Where people differ is in their estimates of the relative amounts. We feel that this can only be decided by experiment.” (Orgel et al. 1980)

One can find examples like this all the way back to the earliest discussions of non-coding DNA. It simply is NOT TRUE that non-coding DNA was dismissed as functionless.

MYTH: JUNK DNA ISN’T JUNK AFTER ALL

Once the vast majority of our DNA was dismissed as junk, but now we know it is important – or so you might have read recently. In fact, it still appears likely that 85 to 95 per cent of our DNA is indeed useless. While many bits of DNA that do not code for proteins are turning out to have some function or other, this was predicted by some all along, and the overall proportion of our DNA with a proven function remains tiny.

It’s especially nice that they cited this blog!

The Cambrian explosion triggered by critical turning point in genome size evolution
Biochem Biophys Res Commun. 2010 Jan 11. [Epub ahead of print]
Li DJ, Zhang S

The Cambrian explosion is a grand challenge to science today and involves multidisciplinary study. This event is generally believed as a result of genetic innovations, environmental factors and ecological interactions, even though there are many conflicts on nature and timing of metazoan origins. The crux of the matter is that an entire roadmap of the evolution is missing to discern the biological complexity transition and to evaluate the critical role of the Cambrian explosion in the overall evolutionary context. Here we calculate the time of the Cambrian explosion by a “C-value clock”; our result quite fits the fossil records. We clarify that the intrinsic reason of genome evolution determined the Cambrian explosion. A general formula for evaluating genome size of different species has been found, by which the genome size evolution can be illustrated. The Cambrian explosion, as a major transition of biological complexity, essentially corresponds to a critical turning point in genome size evolution.

Endogenous (non-retro) virus evolution:

• Original paper
• Not Exactly Rocket Science
• ERV
• NeuroLogica
• The Loom (and NYT)

Substantial differences in Y-chromosomes of humans versus chimps:

• Original paper
• Not Exactly Rocket Science
• John Hawks

Discovery of fossil tetrapod tracks older than previously anticipated:

• Original paper
• Not Exactly Rocket Science
• Pharyngula
• Why Evolution is True

Various visitors to this blog have brought up the hypothesis in one form or another, so even though little or no data is ever presented (and counter-examples are generally dismissed out of hand), I will once again treat the idea seriously.

Specifically, here is my overview of what proponents of the mutation protection hypothesis need to know and what they need to do if they want this to move out of the armchair and into the realm of science.

I. This is not a new idea.
If you have been following this blog, you will know that functions for non-coding DNA have been proposed regularly for decades. Not surprisingly, the notion that it protects genes from mutagens was one of them. This hypothesis dates back in a general form nearly 40 years to the paper in Nature by Yunis and Yasmineh (1971). As they wrote:

“Recent reports indicate that the DNA of constitutive heterochromatin is composed to a large extent of short repeated polynucleotide sequences, termed satellite DNA. This discovery has necessitated a critical review of current ideas concerning the origin and function of this portion of the genome of higher organisms (4-12). A careful appraisal of the information that has accumulated about heterochromatin since the time of Heitz [late 1920s, early 1930s] and on satellite DNA during the last decade suggests that these entities have vital structural functions: they maintain nuclear organization, protect vital regions of the genome, serve as an early pairing mechanism in meiosis, and aid in speciation.”

Yunis and Yasmineh (1971) focused primarily on structural roles for non-coding DNA, and I don’t think aiding in speciation can be considered a “function”, but they did also include the basic notion of genome defense.

True to the standard view of the 1970s (and, to a significant extent, of many authors today), they begin with an adaptationist assumption and build from there:

“With the assumption that a portion that comprises some 10 percent of the genomes in higher organisms cannot be without a raison d’etre, an extensive review led us to conclude that a certain amount of constitutive heterochromatin is essential in multicellular organisms at two levels of organization, chromosomal and nuclear. At the chromosomal level, constitutive heterochromatin is present around vital areas within the chromosomes. Around the centromeres, for example, heterochromatin is believed to confer protection and strength to the centromeric chromatin. Around secondary constrictions, heterochromatic blocks may ensure against evolutionary change of ribosomal cistrons by decreasing the frequency of crossing-over in these cistrons in meiosis and absorbing the effects of mutagenic agents. During meiosis heterochromatin may aid in the initial alignment of chromosomes prior to synapsis and may facilitate speciation by allowing chromosomal rearrangement and providing, through the species specificity of its DNA, barriers against cross-fertilization.”

A few years later — and three years after the rise of the term “junk DNA” (Ohno 1972; Comings 1972) — Hsu (1975) provided a much stronger argument for what he called the “bodyguard hypothesis”. To start, Hsu (1975) noted that many hypotheses had already been presented for the function of heterochromatin, of which he listed six. Importantly, he also noted the following, which seems to have been lost on most current authors:

“Some investigators consider the repeated DNA sequences as the equivalent of ‘appendices’ of gene evolution and therefore facetiously refer to them as ‘junk’. Actually few really think that ‘junk’ DNA is completely useless (cf. Ohno 1972; Comings 1972).”

Now, was Hsu saying that Ohno and Comings did or did not claim that junk DNA is completely useless? The “confer” is ambiguous (it can mean either “compare with” or “consult”), but Hsu was almost certainly aware that Comings was explicit in ascribing function to a large portion of junk DNA.

In any case, the “bodyguard hypothesis” was described as follows:

“The hypothesis proposed here is a simple-minded one: constitutive heterochromatin is used by the cell as a bodyguard to protect the vital euchromatin by forming a layer of dispensable shield on the outer surface of the nucleus. Mutagens, clastogens [inducing chromosome breakage] or even viruses attacking the nucleus must first make contact with the constitutive heterochromatin which absorbs the assault, thus sparing the euchromatic genes from damage, unless the detrimental agents are overpowering.”

Hsu did not apply this to all causes of mutation nor to all types of non-coding DNA — “Probably heterochromatin is ineffective in protecting euchromatic genes against penetrating ionizing radiations, but against chemicals (especially large molecules) and viruses, the layer of thick chromatin may be an excellent barrier” — but it has certainly been invoked more broadly by others since.

For example, the idea has been brought up with renewed vigour by some Russian geneticists (Patrushev 1997; Patrushev and Minkevitch 2006, 2007, 2008). In this case, the focus is on endogenous mutagens (i.e., free oxygen radicals generated through aerobic metabolism). They take this much farther than Hsu by applying it as a major explanation for genome size differences generally and by including transposable elements (which are much more abundant than satellite DNA). As they argued:

“Our data suggest the following molecular mechanism that controls the size of eukaryotic genome in phylogenesis. During the whole life, nuclear DNA of aerobic organisms is affected by a continuous flow of endogenous mutagens. Mutagens escaping the neutralizing effect of antimutagenesis system damage the nucleic bases of DNA, most of which are corrected by repair systems. This ensures a permissible genetically determined level of spontaneous mutagenesis. An increase in the intranuclear concentration of mutagens raises the mutation rate in genome-coding sequences,among which gene(s) of molecular sensor are present. Mutational alterations in the sensor mobilize retrotransposons, which results in a local growth in their copy number, enlargement of genome size, and a decrease inthe mutation in the corresponding coding sequences. As a result, the genome–endogenous mutagen system reaches a new steady-state level. A decrease in the intranuclear concentration of mutagens will be accompanied by a reduction of genome size as a result of spontaneous deletions in its now excessive (in view of accomplishing the protective functions) sequences.” (Patrushev and Minkevitch 2006)

Put more directly, and very much in line with Hsu’s depiction of a “bodyguard”,

“In such a situation, the noncoding DNA of eukaryotic genome behaves quite ‘altruistically’ by putting itself under injuries instead of coding DNA.” (Patrushev and Minkevitch 2008)

The model they propose is summarized in this figure from Patrushev and Minkevitch (2008):

From Patrushev and Minkevitch (2008). Click for larger image.

Hsu (1975) recognized the problem of speculating on functions for junk DNA without evidence or any clear means of empirical testing. Thus, he was careful to provide several specific predictions of his bodyguard hypothesis that are amenable to analysis:

1. “the mutation rate induced by chemical mutagens should be inversely correlated with the number of B chromosomes”.
2. heterochromatin should be “more concentrated at the periphery of the nucleus (and probably also at the nucleoli) than in the interior”.
3. “organisms with more constitutive heterochromatin [should be] more resistant to induced mutations, at least by chemical mutagens”.

Again, let’s take the idea seriously and ask how Hsu’s original predictions have fared over the past 35 years.


Prediction 1: B chromosomes vs. mutation rate
B chromosomes (also called supernumerary chromosomes) are something of an odd choice in this context, because they are not found in all species and they vary in size and number within and among species. By definition, they are not important for survival. They do appear to have effects on recombination (i.e., they increase its frequency), and this has in the past been suggested as a functional role. On the other hand, in high numbers they appear to have deleterious effects on the organisms carrying them. Indeed, B chromosomes were described very early on as parasitic elements (Östergren 1945; one of the first clear expositions of the “selfish DNA” idea), and this remains the most common interpretation (Camacho 2005).

I am not aware of many tests of the prediction that more B chromosomes will provide greater protection against mutations (iperhaps because I don’t follow the B chromosome literature very closely), and in any case the other deleterious impacts and obvious parasitic properties of B chromosomes challenge a primarily adaptive explanation for their presence. However, there are a few experiments that are relevant to this prediction. For example, here is the abstract from a recent study by Weber et al. (2007) on B chromosomes and mutations in maize:

Two hypotheses (the Bodyguard hypothesis and the ABCW hypothesis) have been proposed that predict that the amount and type of chromatin in the nucleus will affect induced mutation rates. The Bodyguard hypothesis proposes that a function of constitutive heterochromatin may be to protect euchromatin from chemical mutagens. The ABCW hypothesis, states that the mutation rate per locus from ionizing radiation is directly proportional to the haploid DNA content of a species. We altered the total amount of genomic DNA and also the amount of heterochromatin by adding supernumerary B chromosomes (which are largely composed of heterochromatin) to maize (Zea mays L.) cells. We compared induced mutation frequencies at the yellow-green2 (yg2) locus in near-isogenic plants that contained 0 (diploid) or 4 supernumerary B chromosomes (diploid + 4 Bs) to evaluate these hypotheses. We found that the chemical mutagen, EMS, caused significantly higher mutation frequencies in plants that contained 4 B chromosomes (and therefore additional constitutive heterochromatin) than in diploid controls. The Bodyguard hypothesis predicts precisely the opposite result. We also found that ionizing radiation caused significantly higher mutation frequencies in plants with 4 B chromosomes than in diploid control plants. This type of change is predicted by the ABCW hypothesis; however, the extent of the increase observed in this study is much higher than the ABCW hypothesis would predict. The higher mutation frequencies from EMS and radiation in plants that contained 4 B chromosomes was unanticipated, and is the first observation that cells may be more susceptible to mutagenesis when B chromosomes are present. We also compared spontaneous mutation frequencies at the waxy1 (wx1) locus in plants containing 0 or 4-5 B chromosomes, and found that the presence of B chromosomes had no detectable impact. However, the pollen abortion frequency was significantly increased by the presence of 5 B chromosomes.

Prediction 2: Arrangement of chromatin
The idea that chromatin is arranged non-randomly in the nucleus is at least 100 years old. Theodor Boveri described chromatin “territories” in 1909, for example. According to Hsu’s hypothesis, heterochromatin should be localized on the outer region of the nucleus as a shield for the sensitive euchromatin in the interior. Again, I do not follow the literature on nuclear structure carefully, but there are some papers that deal with this issue of which I am aware. For example, Tanabe et al. (2002) concluded the following in their study of chromatin arrangement and mutational patterns:

“Evidence for evolutionary conservation argues for a still unknown functional significance of distinct radial higher-order chromatin arrangements. In 1975, T.C. Hsu proposed the ‘bodyguard’ hypothesis for a possible function of constitutive heterochromatin. He argued that constitutive heterochromatin localized in the nuclear periphery might protect the centrally localized euchromatin against mutagens, clastogens, and viruses. However, evidence for the existence of a protection shield has not been provided so far. The fact that later replicating, gene-poor chromatin is incorporated in the constitutive, gene free heterochromatin to form a chromatin shield in the nuclear periphery cannot be easily integrated into this hypothesis. While G-dark band chromatin contains tissue-specific genes, these genes are certainly not of minor importance as compared with the housekeeping genes that are localized in G-light band chromatin in the interior nuclear compartment. The finding in the human fibroblast nuclei that—in contrast to lymphocyte nuclei—both HSA18 and 19 territories are apparently in contact with the nuclear envelope and thus similarly exposed to mutagens, which will enter the nucleus, presents another difficulty. Why should gene dense HSA19 be better protected in lymphocyte nuclei than in fibroblast nuclei? Furthermore, in the light of the bodyguard hypothesis, we would expect to observe DNA damage preferentially in the peripheral chromatin shield. However, several reports indicate a non-random distribution of double strand breaks, as well as endonuclease- or radiation-induced chromosome aberration sites were preferentially observed in the gene-dense G-light bands.”

Again, there may be data out there that support the mutation protection idea, but so far it is not looking good for the hypothesis.


Prediction 3: Non-coding DNA content vs. mutation rate
It is an interesting bit of historical trivia that some early work on genome size diversity was funded by the US Atomic Energy Commission, much as the human genome sequencing initiative was supported by the Department of Energy. In the 1960s and 1970s, there was interest in patterns of sensitivity to radiation and their potential relation to genomic properties including genome size. In general, these studies reported a positive correlation between mutagenic sensitivity to radiation and DNA content (Sparrow and Evans 1961; Sparrow and Miksche 1961; Sparrow et al. 1965, 1968; Baetcke et al. 1967; Abrahamson et al. 1973; Wolff and Abrahamson 1974; Athanasiou and Heddle 1975; Heddle and Athanasiou 1975; Trujillo and Dugan 1975). That is to say, more DNA means more, not less, sensitivity to radiation-induced mutations on a per-locus basis.

From Abrahamson et al. (1973). Click for larger image

From Trujillo and Dugan (1975). Click for larger image.

From Heddle and Athanasiou (1975). Click for larger image.

From Heddle and Athanasiou (1975). Click for larger image.

III. Previous observations need to be explained.
One of the reasons that the mutation protection hypothesis does not have widespread acceptance is that there seem to be too many well-known phenomena that do not jive well with it. Consider the following patterns:

1. Species exposed to intense UV (e.g., on land or in freshwater in the Arctic, pelagic plankton, etc.) do not appear to have large genomes. On the other hand, some very large genomes are found in deep-sea invertebrates.
2. Among vertebrates, species with high metabolic rates, and presumably more free oxygen radicals, have smaller genomes than species with lower metabolic rates.
3. There can be substantial differences in genome size among similar organisms, for example as in onion and its relatives or among salamanders.
4. Despite claims to the contrary based on small and questionable analyses, there are no clear relationships between genome size and lifespan.
5. Transposable elements, which are the primary contributor to genome size, can cause a range of mutations through insertion into genes or by causing large deletions by illegitimate recombination, the latter of which is especially likely with the long terminal repeat (LTR) elements that are common in plants.
6. DNA content obviously can be amplified in somatic cells by endoreduplication, but this tends to be in cells involved in ion exchange, protein production, etc., and not ones exposed most to mutagens (such as the skin exposed to UV).

Conclusions
Overall, the mutation protection idea has intuitive appeal, which is why it was proposed so early and why it continues to pop up as an apparently independent invention among interested non-experts. As I said, I am happy to consider it as a legitimate hypothesis — but only if it moves well beyond the usual pattern in which it is proposed as though it were new, accepted without supporting evidence, and defended through dismissal of obvious counter-evidence. The null hypothesis, that much of the non-coding DNA in eukaryotic genomes does not have an organismal function, also has to be acknowledged as at least equally plausible in light of our understanding of genome biology.

References

Abrahamson, S., M.A. Bender, A.D. Conger, and S. Wolff (1973). Uniformity of radiation-induced mutation rates among different species. Nature 245: 460-462.

Athanasiou, K. and J.A. Heddle (1975). EMS induced mutation rates and their relation to genome size. Canadian Journal of Genetics and Cytology 17: 455.

Baetcke, K.P., A.H. Sparrow, C.H. Nauman, and S.S. Schwemmer (1967). The relationship of DNA content to nuclear and chromosome volumes and to radiosensitivity (LD50). Proceedings of the National Academy of Sciences of the USA 58: 533-540.

Camacho, J.P.M. (2005). B chromosomes. In: The Evolution of the Genome, ed. T.R. Gregory. Elsevier, San Diego, pp.223-286.

Comings, D. E. (1972). “The structure and function of chromatin.” Advances in Human Genetics 3: 237-431.

Heddle, J.A. and K. Athanasiou (1975). Mutation rate, genome size and their relation to the rec concept. Nature 258: 359-361.

Hsu, T.S. (1975). A possible function of constitutive heterochromatin: the bodyguard hypothesis. Genetics 79 (Suppl. 2): 137-150

Ohno, S. (1972). So much “junk” DNA in our genome. Evolution of Genetic Systems. H. H. Smith. New York, Gordon and Breach: 366-370.

Östergren, G. (1945). “Parasitic nature of extra fragment chromosomes.” Botaniska Notiser 2: 157-163.

Patrushev, L.I. (1997). Altruistic DNA: About protective functions of the abundant DNA in the eukaryotic genome and its role in stabilizing genetic information. Biochemistry and Molecular Biology International 41: 851-860

Patrushev, L.I. and I.G. Minkevich (2006). Eukaryotic non-coding DNA sequences provide genes with an additional protection against chemical mutagens. Russian Journal of Bioorganic Chemistry 32: 408-413

Patrushev, L.I. and I.G. Minkevich (2007).Genomic non-coding sequences and the size of eukaryotic cell nucleus as important factors of gene protection from chemical mutagens. Russian Journal of Bioorganic Chemistry 33: 474-477

Patrushev, L.I. and I.G. Minkevich (2008). The problem of eukaryotic genome size. Biochemistry 73: 1519-1552.

Sparrow, A.H. and H.J. Evans (1961). Nuclear factors affecting radiosensitivity. I. The influence of nuclear size and structure, chromosome complement, and DNA content. Brookhaven Symposia in Biology 14: 76-100.

Sparrow, A.H. and J.P. Miksche (1961). Correlation of nuclear volume and DNA content with higher plant tolerance to chronic radiation. Science 134: 282-283.

Tanabe, H., F.A. Habermann, I. Solovei, M. Cremer, and T. Cremer (2002). Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications. Mutation Research 504: 37-45.

Sparrow, A.H., K.P. Baetcke, D.L. Shaver, and V. Pond (1968). The relationship of mutation rate per Roentgen to DNA content per chromosome and to interphase chromosome volume. Genetics 59: 65-78.

Trujillo, R. and V.L. Dugan 1975. Radiosensitivity and radiation-induced mutability: an empirical relationship. Rad. and Environm. Biophys. 12: 253-256.

Vinogradov, A.E. (1998). Buffering: a possible passive-homeostasis role for redundant DNA. Journal of Theoretical Biology 193: 197-199.

Weber, D.F., M.J. Plewa, and R. Feazel (2007). Effect of B chromosomes on induced and spontaneous mutation frequencies in maize. Maydica 52: 109-115.

Wolff, S., S. Abrahamson, M.A. Bender, and A.D. Conger (1974). The uniformity of normalized radiation-induced mutation rates among different species. Genetics 78: 133-134.

Yunis, J.J. and W.G. Yasmineh (1971). Heterochromatin, satellite DNA, and cell function. Science 174: 1200-1209.

Reduced genome works fine with 2000 chunks missing

To put a figure on how much of our DNA is non-essential, Vrijenhoek and his colleagues screened the genomes of 600 healthy students, searching for chunks of DNA at least 10,000 base pairs in length that were missing in some individuals. Across all the genomes, about 2000 such chunks were missing – amounting to about 0.12 per cent of the total genome.

Some people will over-interpret this as strong evidence for a majority of “junk DNA”. Comprising only 0.12% of the genome, it isn’t. However, as these are natural deletions >10kb, it gets around the objections to the deletion studies (i.e., that the conditions in the lab weren’t the same as the challenges faced in the wild). Then again, it may be that you can have one or two deletions and be ok because there is some redundancy, but if you were missing all of these bits you’d be in trouble. Others will dismiss it as an artifact or somehow not really testing the claim (read: dogmatic assumption) that all DNA is functional, but what else is new.

The elements under discussion are endogenous retroviruses (ERVs) which, as the name suggests, are viral-like sequences that exist within the genome. Depending on who you ask, they are either very similar to or are interchangeable with long terminal repeat (LTR) retrotransposons. ERVs make up approximately 8% of the human genome, while LTR elements account for 50-80% of the maize genome.

Endogenous retroviruses were discovered in the 1960s and 1970s (see Weiss 2006), but were first dubbed “endogenous viruses” by David Baltimore in 1974 (published in Baltimore 1975).

Here is how Baltimore (1975) explained their origin:

Evidence has accumulated that viruses have entered the germ line at various times during the ancestry of different species. For convenience, two different cases can be considered: acquisition of viral genomes during inbreeding or domestication and acquisition of viral genomes during the evolution of a species. In principle, viruses could have become part of an animal genome at any stage of evolution and still be detectable now.

Baltimore (1975) discussed the fact that these “endogenous viruses” generally do not grow well in the species in which they had been identified, and that they often show signs of degrading by mutation. Moreover, being clearly similar to viruses and sometimes causing diseases, it seemed very unlikely that they were maintained because they conferred some functional advantage to their hosts. As he concluded,

It is my guess that these viruses have no positive function to play in the life of the animals in which they are resident. Rather, there is an evolutionary equilibrium balancing their acquisition and loss. The viruses are being inserted into the germ line at very low frequency, after which they require many thousands or millions of years to be mutated away because they have little or no detrimental effect on the animal in which they are resident. Viruses that did have a detrimental effect would be lost rapidly and might never come to our attention.

It is worth noting that Baltimore (1975) does not cite Ohno (1972), makes no reference to “junk DNA”, and reaches a tentative conclusion about lack of function from his consideration of the origin and properties of the elements.

Today, some examples are known of ERVs with beneficial effects, such as in placental development (Mi et al. 2000) and p53 binding sites (Wang et al. 2007). (Note, however, that only 0.5% of identified ERVs are associated with binding sites). As Weiss (2006) summarized the present situation:

As Mendelian elements, retroviruses must be subject to host selection. However, with the exception of enrolling env genes in placental differentiation, ERV appear to be parasitic DNA sequences for which the host has little use, other than to protect against further retrovirus infection. Potentially, ERV can damage the host by mutational insertion and by homologous recombination. But despite a tendency to implicate ERV in many ‘non-infectious’ diseases in humans, there is scant evidence that they play a significant role. There are only rare examples where a recessive single gene disorder in a family lineage is caused by an endogenous retroviral insertion disrupting gene function.

Seems like Baltimore’s (1975) assessment was largely correct with regard to mammalian ERV sequences.

_________

Baltimore, D. (1975). Tumor viruses: 1974. Cold Spring Harbor Symposia on Quantitative Biology 39: 1187-1200.

Mi, S. et al. (2000). Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis. Nature 403: 785-789.

Wang, T. et al. (2007). Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proceedings of the National Academy of Sciences USA 104: 18613-18618.

Weiss, R.A. (2006). The discovery of endogenous retroviruses. Retrovirology 3: 67.

____________

Part of the Quotes of interest series.

The elucidation of the evolutionary origins of Alu elements came some time after their initial discovery in 1979. Initially, it was thought that the 7SL RNA gene was derived from Alu, but the reverse conclusion was given by Ullu and Tschudi (1984) and was discussed further by authors such as Quentin (1992). As noted, the original papers reporting the existence of Alu elements raised the question about their potential functions. However, the later articles arrived right in the middle of the supposed time when non-coding DNA was dismissed as irrelevant. Once again, the actual literature from the period does not support the notion that such a dismissal ever actually occurred.

Ullu and Tschudi (1984) did not discuss possible function explicitly, but they did note that “these 7SL-specific homologies may reflect a strong functional constraint acting on these sequences.” In an accompanying article in the same issue of Nature, Brown (1984) was more specific about the significance of the results. He stated,

Ullu and Tschudi suggest that Alu sequences represent defective 7SL RNA molecules that have been reverse-transcribed into DNA and inserted into the genome. An analogous origin has been suggested for alpha-globin pseudogenes in the mouse, and the multiple pseudogenes for small nuclear RNAs in man. Pseudogenes are generally thought not to play an important role in the cell. Perhaps those who have argued that Alu, by its very abundance, must have an important function will recognize that this argument has now lost some of its weight.

Two important things are expressed here. One, the assumption that Alu elements are functional because they are abundant (i.e., an adaptationist expectation that they would have been removed otherwise) was apparently common in the early 1980s. Indeed, that’s why the “selfish DNA” idea was proposed (Orgel and Crick 1980; Doolittle and Sapienza 1980). Two, pseudogenes — defunct coding genes — were indeed thought to be non-functional, for obvious reasons. These are the sequences to which the term “junk DNA” originally related.

Additional information regarding the origin of Alu sequences was provided by Quentin (1992), who said,

from the beginning, the Alu progenitor sequences could have retained the capacity to interact with cellular components, suggesting that they are functionally important for the host genome. On the other hand, this RNA secondary structure could have some affinity for reverse transcriptases or other components of the retroposition machinery, and its conservation in the monomeric and Alu dimeric sequences could be related to their mobility. Indeed, this structure is first found in the 7SL RNA sequences that are prone to retroposition, and it is also retained by the progenitor sequences of the Bl family in the rodent genomes. Nevertheless, both hypotheses (secondary structure involved in a cellular function or in the reverse transcription) are not mutually exclusive.

Yet, here is a fairly typical introduction from a recent paper about Alu (Hasler and Strub 2006):

Alu elements, as well as other repetitive elements, were at the origin considered as parasites of the genome that had no major effect on its stability and genic expression. They were thought to be ‘selfish’ or ‘junk’DNA (6,7), but nowadays, several lines of evidence show that the presence of repetitive elements and especially of Alu elements, had a great influence on the human genome, in particular on its evolution. These effects were both negative and positive. On one hand, integration into genic regions that caused gene inactivation might often have been deleterious for the organism. On the other hand, because of their extended sequence homology, Alu elements induced a considerable number of non-allelic recombinations that lead to both duplications and deletions of DNA segments, thereby accelerating evolution by several orders of magnitude. Another function frequently attributed to Alu elements is their ability to provide new regulatory elements to neighboring genes. It was, indeed, reported several times that Alu elements became effectors of gene transcription by providing new enhancers, promoters and polyadenylation signals to many genes.

The only authors cited for the “Alu is just junk” are Orgel and Crick (1980) and Orgel et al. (1980). I have discussed these articles before, but will reiterate one statement from each.

Orgel and Crick (1980):

It would be surprising if the host genome did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use … would be for control purposes at one level or another.

Orgel et al. (1980):

In our recent experience most people will agree, after discussion, that ignorant DNA, parasitic DNA, symbiotic DNA (that is, parasitic DNA which has become useful to the organism) and ‘dead’ DNA of one sort or another are all likely to be present in the chromosomes of higher organisms. Where people differ is in their estimates of the relative amounts. We feel that this can only be decided by experiment.

______

Part of the Quotes of interest series.
______

References

Brown, A.L. 1984. On the origin of the Alu family of repeated sequences. Nature 312: 106.

Hasler, J. and K. Strub. 2006. Alu elements as regulators of gene expression. Nucl. Acids Res. 34: 5491-5497.

Orgel, L.E. and F.H.C. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.

Orgel, L.E., F.H.C. Crick, and C. Sapienza. 1980. Selfish DNA. Nature 288: 645-646.

Quentin, Y. 1992. Origin of the Alu family: a family of Alu-like monomers gave birth to the left and right arms of the Alu elements. Nucl. Acids Res. 20: 3397-3401.

Ullu, E. and C. Tschudi. 1984. Alu sequences are processed 7SL RNA genes. Nature 312: 171-172.

As mentioned previously, satellite DNAs were discovered in the early 1960s, and by the late 1960s and early 1970s there was substantial interest in these highly repetitive components of the genome. Nature published several stories about this work in their “News and Views” section, authored by various unnamed correspondents. Of course, one must not take the interpretation of anonymous science writers as definitive (after all, their contemporary counterparts do much to add the the mythology surrounding noncoding DNA), but it supports the overall contention that during this period adaptationist thinking was dominant and thus that it was taken almost as a given that functions would be elucidated for noncoding sequences. You will notice also that many of these stories report on data that contradict proposed functions, yet the expectation remained that some function exists. I am not criticizing the studies of these early authors in any way. Some satellite DNA is functional in chromosomal structure, but the point is that at the time this was an a priori assumption rather than a conclusion, and it is clearly not the case that these elements were dismissed as unimportant.

“Mouse satellite DNA”, Nature 215: 575, August 5, 1967:

What is the function of satellite DNA? It is unlikely to code for protein and yet it forms 10 per cent of the cell’s total DNA. What possible purpose is served by having so many, apparently identical, short sequences within the same genome?

“Satellite DNA”, Nature 222: 327, April 26, 1969:

Unfortunately, the group’s latest data serve only to make ideas about the function of this strange DNA fraction even more obscure.

…

But if satellite DNA is not transcribed, what is its function? Flamm et al. are impressed by the fact that numerous copies of a nucleotide sequence of 350 bases have been maintained during evolution in the face of the tendency to accumulate random mutations. This implies that satellite DNA has some important function. They suggest that it is required for “housekeeping”, the folding and packing of DNA in the chromosomes. In the absence of any critical data or any way of testing for the function of this DNA, that is as good a suggestion as any.

…

Like the Edinburgh group, Maio and Schildkraut are convinced that satellite DNA has some vital, albeit unknown, function.

“Hybridization and satellite DNA”, Nature 225: 414, January 31, 1970:

The function of this satellite DNA has always been obscure, reducing investigators to suggest, for example, that it may be involved in chromosome “housekeeping”, but Pardue and Gall claim that it is localized in the centromeres. It may therefore play a role in chromosome pairing, and this may account for the curious properties of satellite DNA, not least its peculiar base sequence.

“Mysterious satellites”, Nature 225: 899-900, March 7, 1970:

Any biologist told that 10 to 12 percent of the total DNA genome of an animal is sequestered in a chemically distinct fraction would find it hard to escape the conclusion that such DNA has some crucial cellular function. That explains why the so-called satellite DNAs are exciting so much interest…

…

A host of experiments and speculations leap to mind. Perhaps satellite DNA plays some part in the assembly of the mitotic spindle, for example, by influencing polymerization of spindle protein or the attachment of chromosomes to the spindle. Hybrid cells might be useful in studying the specificity of a putative interaction between satellite DNA and components of the mitotic spindle. And the chromosomes of organisms with diffuse centromeres might be useful for further testing the relationship between satellite DNA and centromeres.

The last one is interesting, because it led to a correction by one of the first people to identify satellite DNA, Waclaw Szybalski, in the correspondence segment of the April 4, 1970 issue. Did he complain about the characterization of biologists anticipating functions for satellite DNA? No, he simply noted that the author got the date of discovery wrong (Szybalski 1970; Nature 226: 89-90).

“Satellite DNA and sequence”, Nature 227: 775, August 22, 1970:

What possible function can be served by a DNA which consists of tandem duplication of a sequence of only six base pairs, and why should an animal such as the guinea-pig require some 10⁷ copies of this short sequence in all its cells?

…

Finally, even though we now know the basic sequence unit of a satellite DNA we are no closer to explaining the function of these specialized DNAs. Since they have no role in coding protein, the most plausible suggestion is that they have some role in maintaining the integrity of the chromosome itself. The localization of satellite DNA in the centromere regions of chromosomes suggests they play a part in the functions conventionally ascribed to the centromere. But for the time being such suggestions remain speculative.

“Satellite DNA and speciation”, Nature 240: 128, November 17, 1972:

The function and evolutionary significance of satellite DNA — DNA which has a reiterated base sequence, is associated with heterochromatin and centromeres and may or may not be transcribed — remain tantalizing mysteries. It seems unlikely that these simple sequences code for any polypeptides and it has, therefore, been suggested that satellite DNA may be involved in processes such as pairing of homologous chromosomes, chromosome movement and chromosome packing, but there is little evidence in support of these speculations.

“The mystery deepens”, Nature 240: 255, December 1, 1972:

But the fact remains that one is still at a loss as to the function of satellite DNA, the chief characteristic of which is its comparatively simple and highly reiterated base sequence, and indeed the more that is learnt about the distribution of satellite DNAs the deeper the enigma of its function becomes.

“DNA dominant at Berkeley, California”, Nature 245: 183-184, September 28, 1973:

The problem of DNA redundancy continues to intrigue several teams, without finally yielding all the secrets of its function or the reason for the wide variation in amount from species to species. Some of the extra DNA is almost certainly present as spacer sequences between cistrons, but this does not account for the large amount of simple sequence DNA, present in millions of copies, in the centromeric heterochromatin. P.M.B. Walker, for whom the Medical Research Council has recently set up a unit in Edinburgh specifically devoted to research on the mammalian genome, reviewed the history of satellite DNA, but said that most investigators would still go no further than suggest that this material, which is not transcribed, has some “housekeeping” function.

Here is the take-home message. From the time it was discovered, satellite DNA was presumed to be functional on the basis of Darwinian adaptationist expectations. This stimulated intensive research on the subject which was considered interesting enough to be reported about regularly in Nature. Some of the proposed functions, such as a structural role for some noncoding sequences, turned out to be correct — which was only shown because the Darwinian assumption prompted researchers to test functional ideas. The claim by creationists that “Darwinism” prevented such research is manifestly and demonstrably inaccurate. The problem, as I have noted, is that a strict focus on adaptive roles for noncoding DNA prevented many researchers from adopting a more balanced approach under which some of it is functional but most of it is not.

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Part of the Quotes of interest series.

I have already mentioned Alu elements — by far the most common single type of noncoding DNA element in the human genome. Alu elements are part of the category of repetitive DNA known as SINEs, which stands for short interspersed repeated sequences (or short interspersed nuclear elements). These sequences are now recognized as a type of transposable element that uses an RNA intermediate (i.e., undergoes retrotransposition) but which cannot do so without borrowing (some say parasitizing) the molecular transposition apparatus of other elements, namely long interspersed repeated sequences (LINEs). LINEs are not as common in the human genome as SINEs, but as they are much larger, they make up more of the total DNA. Whereas there are about 1.5 million SINEs (1 million of them Alu) making up about 13% of the genome sequence, the 870,000 or so copies of LINE elements (more than 500,000 of them LINE-1) constitute more than 20% of human DNA.

The terms SINE and LINE were coined by Maxine Singer in 1982 (Singer 1982a). By that time, the term “junk DNA” (Ohno 1972; Comings 1972) had been in circulation for a decade, and this was also two years after the “selfish DNA” hypothesis was put forward by Orgel and Crick (1980) and Doolittle and Sapienza (1980). Singer (1982b) cited these latter papers (but not Ohno’s) in her longer review of mammalian repeated DNA sequences. So once again, we have a prime candidate for assessing the general attitude in the scientific community regarding possible function of noncoding DNA sequences during the supposed period of neglect.

Were SINEs and LINEs dismissed as mere junk unworthy of further exploration?

Singer (1982a):

Function?
The critical question about SINEs and LINEs concerns their function, if they have any. The catalog of proposed functions for SINEs includes many of the unsolved problems in molecular biology, but none has been demonstrated directly. The existence of RNA transcripts from some SINE-family members is the most compelling argument available that they have a function, although functions independent of transcription (and in addition to transposition) have also been suggested. (The possibility that LINEs are transcribed requires investigation). Particularly striking is the fact that the 4.5S transcripts of Alu-like SINEs of hamster and mice are more than 95% identical in sequence, which is significantly closer than the variation among the different copies of a SINE family in a single species. If we assume that one or a few SINEs encode the 4.5S RNAs, is there any functional significance to the many other dispersed copies of family members? It seems reasonable to expect that there is some trade-off between an advantage imparted to cells by SINEs and the disadvantage of a promiscuous and abundant mobile element that is presumably destructive if implanted in an essential coding region.

Singer (1982b):
[A number of in-line citations have been omitted for clarity]

Are SINES functional?
As a background, it is interesting to recall proposals suggesting that highly repeated dispersed sequences may be without function (Orgel and Crick 1980; Doolittle and Sapienza 1980) and also disagreement concerning those proposals (Cavalier-Smith 1980; Dover 1980; T.F. Smith 1980; Orgel et al. 1980; Dover and Doolittle 1980). Specific functions that have been suggested include the control of gene expression, perhaps by involvement of transcripts of SINES in the maturation of messenger RNA, and service as origins of DNA replication.

…

The following additional point may be important, in view of the suggestions that highly repeated sequences have no function at all. A mobile element may generate diversity with a potential selective advantage, but it can also generate disadvantage if it moves into an essential gene. Mutation by movable elements has been demonstrated in yeast and Drosophila. The high frequency of mutation caused by the presence of large numbers of movable elements within a mammalian genome might have proven intolerable and been selected against, unless it was counterbalanced by some positive functional advantage.

Finally, the suggestion that SINES may serve as origins for DNA replication should be considered. The basis for the suggestion is the presence in SINES of a short (14bp) homology to a sequence associated with the origin of replication of murine and primate popaviruses. Georgiev et al. (1981) describe some preliminary experiments that are consistent with this suggestion. However, in popavirus genomes this region is part of a complex control region and may be involved in the control of transcription as well as replication. Only additional experiments will resolve these questions.

…

Are LINES functional?
The discovery of LINE families in mammals is recent and there is very little information available regarding function. Adams et al. (1980) found no transcripts homologous to the human Kpn-LINE family in bone marrow cells and Manuelidis [1982] also reports negative preliminary experiments. There is no information available regarding the possibility that LINES are mobile in mammalian genomes.

As noted previously, the SINE Alu was first described in 1979, and the first LINEs were discovered using similar methods around 1980. Singer (1982b) cites several publications and articles in press detailing sequences of this type from the human and mouse genomes. Most of these papers did not include any discussion one way or the other about function and focused instead on the technique used or the specific molecular characteristics of the sequences. However, one of the early papers did discuss function (and non-function).

Adams et al. (1980):

As to the function or genesis of this sequence we can make only vague hypotheses. The fact that it is not expressed into RNA, at least in bone marrow cells, at levels proportionate to its reiteration frequency, suggests that it does not code for a protein or major nuclear RNA in this tissue. However, there may be a low-level transcript which has some functional role, or there may be transcription in some other tissue. Alternatively this sequence may be a binding site for a chromosomal protein, or serve as a signal for chromosomal folding. As such it could conceivably have some role in the regulation of expression of the β-globin or other nearby genes. The interspersion of this sequence among other DNA is consistant with but not by itself supportive of such a role. Finally it is possible that this repeated sequence has no function relevant to the organism, but is carried in the genome in an essentially parasitic fashion (Doolittle and Sapienza 1980).

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Part of the Quotes of interest series.
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References cited

Adams, J.W., R.E. Kaufman, P.J. Kretschmer, M. Harrison, and A.W. Nienhuis. 1980. A family of long reiterated DNA sequences, one copy of which is next to the human beta globin gene. Nucleic Acids Research 8: 6113-6128.

Cavalier-Smith, T. 1980. How selfish is DNA? Nature 285: 617-618.

Comings, D.E. 1972. The structure and function of chromatin. Advances in Human Genetics 3: 237-431.

Doolittle, W.F. and C. Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.

Dover, G. and W.F. Doolittle. 1980. Modes of genome evolution. Nature 288: 646-647.

Georgiev, G.P., Y.V. Ilyin, V.G. Chmeliauskaite, A.P. Ryskov, D.A. Kramerov, K. G. Skryabin, A. S. Krayev, E. M. Lukanidin, and M. S. Grigoryan. 1981. Mobile dispersed genetic elements and other middle repetitive DNA sequences in the genomes of Drosophila and mouse: transcription and biological significance. Cold Spring Harbor Symposia on Quantitative Biology 45: 641-654.

Manuelidis, L. 1982. Repeated DNA sequences and nuclear structure. In Genome Evolution (eds. G. Dover and A. Flavell), pp. 263-285. Academic Press, New York.

Ohno, S. 1972. So much “junk” DNA in our genome. In Evolution of Genetic Systems (ed. H.H. Smith), pp. 366-370. Gordon and Breach, New York.

Orgel, L.E. and F.H.C. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.

Orgel, L.E., F.H.C. Crick, and C. Sapienza. 1980. Selfish DNA. Nature 288: 645-646.

Singer, M.F. 1982a. SINEs and LINEs: highly repeated short and long interspersed sequences in mammalian genomes. Cell 28: 433-434.

Singer, M.F. 1982b. Highly repeated sequences in mammalian genomes. International Review of Cytology 76: 67-112.

Smith, T.F. 1980. Occam’s razor. Nature 285: 620.